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Yorodumi- PDB-3inj: Human Mitochondrial Aldehyde Dehydrogenase complexed with agonist... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3inj | ||||||
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Title | Human Mitochondrial Aldehyde Dehydrogenase complexed with agonist Alda-1 | ||||||
Components | Aldehyde dehydrogenase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / ALDH / E487K / Rossmann fold / Alda-1 / activator / Mitochondrion / NAD / Transit peptide | ||||||
Function / homology | Function and homology information Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase activity / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation ...Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase activity / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation / carboxylesterase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / Smooth Muscle Contraction / NAD binding / electron transfer activity / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.688 Å | ||||||
Authors | Perez-Miller, S. / Hurley, T.D. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Alda-1 is an agonist and chemical chaperone for the common human aldehyde dehydrogenase 2 variant. Authors: Perez-Miller, S. / Younus, H. / Vanam, R. / Chen, C.H. / Mochly-Rosen, D. / Hurley, T.D. #1: Journal: Science / Year: 2008 Title: Activation of Aldehyde Dehydrogenase-2 Reduces Ischemic Damage to the Heart Authors: Chen, C.H. / Budas, G.R. / Churchill, E.N. / Disatnik, M.H. / Hurley, T.D. / Mochly-Rosen, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3inj.cif.gz | 832.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3inj.ent.gz | 701.7 KB | Display | PDB format |
PDBx/mmJSON format | 3inj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/3inj ftp://data.pdbj.org/pub/pdb/validation_reports/in/3inj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 54499.629 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: lacks mitochondrial leader sequence / Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / Plasmid: pT-7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05091, aldehyde dehydrogenase (NAD+) |
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-Non-polymers , 5 types, 4050 molecules
#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GAI / #5: Chemical | ChemComp-BXB / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.74 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 6.4 Details: 100 MM ACES (N-[2-ACETAMIDO]-2-AMINOETHANE SULFONIC ACID), 10MM MGCL2, 100 MM GUANIDINE HCL, 16-17% W/V PEG 6000, 8MM DTT, pH 6.4, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.07 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2008 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection twin | Operator: l,-k,h / Fraction: 0.278 |
Reflection | Resolution: 1.69→50 Å / Num. obs: 375531 / % possible obs: 93.1 % / Observed criterion σ(I): 0.2 / Redundancy: 2.7 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1.035 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.69→1.75 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.7 / Num. unique all: 36519 / Χ2: 0.863 / % possible all: 90.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.688→46.357 Å / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0.07 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.071 Å2 / ksol: 0.318 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.56 Å2 / Biso mean: 19.786 Å2 / Biso min: 9.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.688→46.357 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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